published papers

Ballgown bridges the gap between transcriptome assembly and expression analysis (Nature Biotechnology, 2015). Again there's code to reproduce results in the paper and software. The paper itself isn't open-access, but there's a free preprint.

DER Finder, or more formally, "Differential expression analysis of RNA-seq data at single-base resolution" (Biostatistics, 2014). There's code that would reproduce the paper several years ago. We also wrote a new and improved version of DER Finder in Nucleic Acids Research in 2016.

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets (BMC Bioinformatics, 2011). An updated version is coming out in 2017 in Nature Biotechnology!

some of my favorite writing by other people

The Night Watch, by James Mickens (Usenix magazine, November 2013). I would highly recommend reading everything James Mickens has written if you're the type of person that enjoys extremely funny writing about computers.